h264 to ProRes problems

Here's my current situation: I have 100Gb of material on h264, shot using a Canon 5dM2 camera. I want it converted to ProRes so I can do post work. If I do this convertion using Compressor, from h264 directly to ProRes, I get heavily altered images. By heavily I mean a 3 to 5% change in luminance (dark images).

If, however, I convert a h264 clip to an Uncompressed 10-bit clip, then take the uncompressed clip and convert it to ProRes, I get a perfect copy.

This poses a bit of a problem, for converting 100Gb of 1920x1280 30fps video to Uncompressed takes a LOT of time and disk space, and I'm supposed to keep shooting with this camera.